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Prof. Dr. Karsten Borgwardt

Adresse: Spemannstr. 41
72076 Tübingen

 

Bild von Borgwardt, Karsten, Prof. Dr.

Karsten Borgwardt

Position: Leiter Forschungsgruppe  Abteilung: 

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Artikel (16):

Song L, Smola A, Gretton A, Bedo J und Borgwardt K (Mai-2012) Feature Selection via Dependence Maximization Journal of Machine Learning Research 13 1393-1434.
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Karaletsos T, Stegle O, Dreyer C, Winn J und Borgwardt KM (April-2012) ShapePheno: Unsupervised extraction of shape phenotypes from biological image collections Bioinformatics 28(7) 1001-1008.
Gretton A, Borgwardt K, Rasch M, Schölkopf B und Smola A (März-2012) A Kernel Two-Sample Test Journal of Machine Learning Research 13 723−773.
Becker C, Hagmann J, Müller J, Koenig D, Stegle O, Borgwardt K und Weigel D (Dezember-2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome Nature 480(7376) 245-249.
Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Müller J, Alonso-Blanco C, Borgwardt K, Schmid KJ und Weigel D (Oktober-2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations Nature Genetics 43(10) 956–963.
Shervashidze N, Schweitzer P, van Leeuwen EJ, Mehlhorn K und Borgwardt M (September-2011) Weisfeiler-Lehman Graph Kernels Journal of Machine Learning Research 12 2539−2561.
Kam-Thong T, Czamara D, Tsuda K, Borgwardt K, Lewis CM, Erhardt-Lehmann A, Hemmer B, Rieckmann P, Daake M, Weber F, Wolf C, Ziegler A, Pütz B, Holsboer F, Schölkopf B und Müller-Myhsok B (April-2011) EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units European Journal of Human Genetics 19(4) 465-471.
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Thoma M, Cheng H, Gretton A, Han J, Kriegel H-P, Smola AJ, Song L, Yu PS, Yan X und Borgwardt KM (Oktober-2010) Discriminative frequent subgraph mining with optimality guarantees Statistical Analysis and Data Mining 3(5) 302–318.
Camps-Valls G, Shervashidze N und Borgwardt K (Oktober-2010) Spatio-Spectral Remote Sensing Image Classification With Graph Kernels IEEE Geoscience and Remote Sensing Letters 7(4) 741-745.
Stegle O, Denby KJ, Cooke EJ, Wild DL, Ghahramani Z und Borgwardt KM (Mai-2010) A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series Journal of Computational Biology 17(3) 355-367.
Stegle O, Drewe P, Bohnert R, Borgwardt K und Rätsch G (Mai-2010) Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts Nature Precedings 2010 1-11.
Lippert C, Ghahramani Z und Borgwardt KM (April-2010) Gene function prediction from synthetic lethality networks via ranking on demand Bioinformatics 26(7) 912-918.
Vishwanathan SVN, Schraudolph NN, Kondor R und Borgwardt KM (April-2010) Graph Kernels Journal of Machine Learning Research 11 1201−1242.
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Pain A, Böhme U, Berry AE, Mungall K, Finn RD, Jackson AP, Mourier T, Mistry J, Pasini EM, Aslett MA, Balasubrammaniam S, Borgwardt K, Brooks K, Carret C, Carver TJ, Cherevach I, Chillingworth T, Clarke T, Galinski MR, Hall N, Harper D, Harris D, Hauser H, Ivens A, Janssen CS, Keane T, Larke N, Lapp S, Marti M, Moule S, Meyer IM, Ormond D, Peters N, Sanders M, Sanders T, Sergeant TJ, Simmonds M, Smith F, Squares R, Thurston S, Tivey AR, Walker D, White B, Zuiderwijk E, Churcher C, Quail MA, Cowman AF, Turner CMR, Rajandream MA, Kocken CHM, Thomas AW, Newbold C, Barrell BG und Berriman M (Oktober-2008) The genome of the simian and human malaria parasite Plasmodium knowlesi Nature 455(7214) 799-803.
Borgwardt K (August-2008) Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model BioEssays 30(8) 707–710.
Vishwanathan SVN, Borgwardt KM, Guttman O und Smola AJ (März-2006) Kernel extrapolation Neurocomputing 69(7-9) 721-729.

Beiträge zu Tagungsbänden (30):

Stegle O, Lippert C, Mooij J, Lawrence N und Borgwardt K (Januar-2012) Efficient inference in matrix-variate Gaussian models with iid observation noise In: Advances in Neural Information Processing Systems 24, , Twenty-Fifth Annual Conference on Neural Information Processing Systems (NIPS 2011), Curran, Red Hook, NY, USA, 630-638.
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Achlioptas P, Schölkopf B und Borgwardt K (August-2011) Two-locus association mapping in subquadratic time, 17th ACM SIGKKD Conference on Knowledge Discovery and Data Mining (KDD 2011), ACM Press, New York, NY, USA, 726-734.
Li L, Rakitsch B und Borgwardt K (Juli-2011) ccSVM: correcting Support Vector Machines for confounding factors in biological data classification, 19th International Conference on Intelligent Systems for Molecular Biology (ISMB 2011), Bioinformatics, 27(13), i342-i348.
Kam-Thong T, Pütz B, Karbalai N, Müller−Myhsok B und Borgwardt K (Juli-2011) Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs, 19th International Conference on Intelligent Systems for Molecular Biology (ISMB 2011), Bioinformatics, 27(13), i214-i221.
Wackersreuther B, Wackersreuther P, Oswald A, Böhm C und Borgwardt KM (Juli-2010) Frequent subgraph discovery in dynamic networks, 155-162, ACM Press, New York, NY, USA, Eighth Workshop on Mining and Learning with Graphs (MLG '10).
Shervashidze N und Borgwardt KM (April-2010) Fast subtree kernels on graphs In: Advances in Neural Information Processing Systems 22, , 23rd Annual Conference on Neural Information Processing Systems (NIPS 2009), Curran, Red Hook, NY, USA, 1660-1668.
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Stegle O, Denby KJ, Wild DL, McHattie S, Mead A, Ghahramani Z und Borgwardt KM (September-2009) Discovering Temporal Patterns of Differential Gene Expression in Microarray Time Series, German Conference on Bioinformatics (GCB 2009), Gesellschaft für Informatik, Bonn, Germany, 133-142.
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Kondor R, Shervashidze N und Borgwardt KM (Juni-2009) The graphlet spectrum, 26th International Conference on Machine Learning (ICML 2009), ACM Press, New York, NY, USA, 529-536.
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Stegle O, Denby K, Wild DL, Ghahramani Z und Borgwardt KM (Mai-2009) A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series In: Research in Computational Molecular Biology, , 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009), Springer, Berlin, Germany, 201-216, Series: Lecture Notes in Computer Science ; 5541.
Thoma M, Cheng H, Gretton A, Han J, Kriegel H-P, Smola AJ, Song L, Yu PS, Yan X und Borgwardt KM (Mai-2009) Near-optimal supervised feature selection among frequent subgraphs, Ninth SIAM International Conference on Data Mining (SDM 2009), Society for Industrial and Applied Mathematics, Philadelphia, PA, USA, 1076-1087.
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Lippert C, Stegle O, Ghahramani Z und Borgwardt KM (April-2009) A kernel method for unsupervised structured network inference, Twelfth International Conference on Artificial Intelligence and Statistics (AISTATS 2009), International Machine Learning Society, Madison, WI, USA, 368-375, Series: JMLR Workshop and Conference Proceedings ; 5.
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Shervashidze N, Vishwanathan SVN, Petri TH, Mehlhorn K und Borgwardt KM (April-2009) Efficient Graphlet Kernels for Large Graph Comparison, Twelfth International Conference on Artificial Intelligence and Statistics (AISTATS 2009), International Machine Learning Society, Madison, WI, USA, 488-495, Series: JMLR Workshop and Conference Proceedings ; 5.
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Hübler C, Kriegel H-P, Borgwardt K und Ghahramani Z (Dezember-2008) Metropolis Algorithms for Representative Subgraph Sampling, 8th IEEE International Conference on Data Mining (ICDM 2008), IEEE, Piscataway, NJ, USA, 283-292.
Song L, Smola AJ, Borgwardt K und Gretton A (September-2008) Colored Maximum Variance Unfolding In: Advances in neural information processing systems 20, , Twenty-First Annual Conference on Neural Information Processing Systems (NIPS 2007), Curran, Red Hook, NY, USA, 1385-1392.
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Kondor R und Borgwardt K (Juli-2008) The skew spectrum of graphs, 25th International Conference on Machine Learning (ICML 2008), ACM Press, New York, NY, USA, 496-503.
Gretton A, Borgwardt KM, Rasch M, Schölkopf B und Smola A (September-2007) A Kernel Method for the Two-Sample-Problem In: Advances in Neural Information Processing Systems 19, , Twentieth Annual Conference on Neural Information Processing Systems (NIPS 2006), MIT Press, Cambridge, MA, USA, 513-520.
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Huang J, Smola A, Gretton A, Borgwardt KM und Schölkopf B (September-2007) Correcting Sample Selection Bias by Unlabeled Data In: Advances in Neural Information Processing Systems 19, , Twentieth Annual Conference on Neural Information Processing Systems (NIPS 2006), MIT Press, Cambridge, MA, USA, 601-608.
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Vishwanathan SVN, Borgwardt KM und Schraudolph N (September-2007) Fast Computation of Graph Kernels In: Advances in Neural Information Processing Systems 19, , Twentieth Annual Conference on Neural Information Processing Systems (NIPS 2006), MIT Press, Cambridge, MA, USA, 1449-1456.
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Gretton A, Borgwardt KM, Rasch M, Schölkopf B und Smola AJ (Juli-2007) A Kernel Approach to Comparing Distributions, Twenty-Second AAAI Conference on Artificial Intelligence (IAAI-07), AAAI Press, Menlo Park, CA, USA, 1637-1641.
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Song L, Bedo J, Borgwardt KM, Gretton A und Smola A (Juli-2007) Gene selection via the BAHSIC family of algorithms, 15th International Conference on Intelligent Systems for Molecular Biology (ISMB 2007), Bioinformatics, 23(13), i490-i498.
Song L, Smola AJ, Gretton A und Borgwardt KM (Juni-2007) A Dependence Maximization View of Clustering, 24th Annual International Conference on Machine Learning (ICML 2007), ACM Press, New York, NY, USA, 815-822.
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Song L, Smola AJ, Gretton A, Borgwardt KM und Bedo J (Juni-2007) Supervised Feature Selection via Dependence Estimation, 24th Annual International Conference on Machine Learning (ICML 2007), ACM Press, New York, NY, USA, 823-830.
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Borgwardt KM, Vishwanathan SVN, Schraudolph N und Kriegel H-P (Januar-2007) Graph kernels for disease outcome prediction from protein-protein interaction networks, Pacific Symposium on Biocomputing (PSB 2007), World Scientific, Hackensack, NJ, USA, 4-15.
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Borgwardt KM, Kriegel H-P und Wackersreuther P (Dezember-2006) Pattern Mining in Frequent Dynamic Subgraphs, Sixth International Conference on Data Mining (ICDM 2006), IEEE Computer Society, Los Alamitos, CA, USA, 818-822.
Assfalg J, Borgwardt KM und Kriegel H-P (November-2006) 3DString: a feature string kernel for 3D object classification on voxelized data, 15th ACM International Conference on Information and Knowledge Management (CIKM 2006), ACM Press, New York, NY, USA, 198-207.
Borgwardt KM, Gretton A, Rasch M, Kriegel H-P, Schölkopf B und Smola A (August-2006) Integrating Structured Biological data by Kernel Maximum Mean Discrepancy, 14th International Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Bioinformatics, 22(14), e49-e57.
Borgwardt KM, Vishwanathan SVN und Kriegel H-P (Januar-2006) Class prediction from time series gene expression profiles using dynamical systems kernels, Pacific Symposium on Biocomputing (PSB 2006), World Scientific, Singapore, 547-558.
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Borgwardt KM und Kriegel H-P (November-2005) Shortest-path kernels on graphs, Fifth International Conference on Data Mining (ICDM 2005), IEEE Computer Society, Los Alamitos, CA, USA, 74-81.
Borgwardt KM, Ong CS, Schönauer S, Vishwanathan SVN, Smola AJ und Kriegel H-P (Juni-2005) Protein function prediction via graph kernels, 13th International Conference on Intelligent Systems for Molecular Biology (ISMB 2005), Bioinformatics, 21(Supplement 1), i47-i56.
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Borgwardt KM, Guttman O, Vishwanathan SVN und Smola AJ (April-2005) Joint Regularization, 13th European Symposium on Artificial Neural Networks (ESANN 2005), D-Side, Evere, Belgium, 455-460.
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Beiträge zu Büchern (2):

Borgwardt KM: Kernel Methods in Bioinformatics, 317-334. In: Handbook of Statistical Bioinformatics, (Ed) H.H.-S. Lu, Springer, Berlin, Germany, (2011).
Gretton A, Smola AJ, Huang J, Schmittfull M, Borgwardt KM und Schölkopf B: Covariate Shift by Kernel Mean Matching, 131-160. In: Dataset Shift in Machine Learning, (Ed) J. Quiñonero Candela, MIT Press, Cambridge, MA, USA, (Februar-2009).
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Technische Berichte (1):

Gretton A, Borgwardt K, Rasch M, Schölkopf B und Smola A: A Kernel Method for the Two-sample Problem, 157, Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany, (April-2008).
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Poster (6):

Drewe P, Stegle O, Bohnert R und Borgwardt K (Juli-2011): Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts, 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2011), Wien, Austria.
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Last updated: Montag, 22.05.2017